Table 1 Common questions about protein structures biologists seek to answer and the visual encoding and/or panel used in the Aquaria user interface to address these.
From: Integrated visual analysis of protein structures, sequences, and feature data
No. | Question | Visual Encoding and/or Panel |
|---|---|---|
1 | For a given protein sequence, how many related 3D structures are known? | Matching Structures (= MS) |
2 | Do any structures match exactly? If not, what is the best match? | vertical position & colour-code (MS) |
3 | Which structure spans most of the given sequence? | horizontal position (MS) |
4 | Which molecular states occur amongst all related structures? | thumbnails (MS) |
5 | For a given domain, how many related structures are known? | horizontal position (MS) |
6 | For a given domain, do any structures match exactly? If not, what is the best match? | position & colour-code (MS) |
7 | For a given domain, which molecular configurations occur in the related structures? | tree level 1 (MS) |
8 | For a given domain and molecular configuration, which PDB entries are related? | tree level 2 (MS) |
9 | In a large molecular assembly, where is a given protein? How does it interact with others? | semi-transparency (3D Structure) |
10 | How well does a structure match to a given protein sequence? | colour-code (3D Structure) |
11 | Which residues in the structure differ from the specified protein sequence? | colour-code (3D Structure) |
12 | Which residues in the structure differ in a related organism (e.g., in mouse)? | colour-code (3D Structure) |
13 | For a given residue in the structure, where is it in the sequence? | 3D Structure |
14 | For a given residue in the sequence, where is it in the structure? | 3D Structure |
15 | Where in the structure is the N-terminus? Where is the C-terminus? | 3D Structure |
16 | Which residues make contact with ligands? Or with other proteins? | 3D Structure |
17 | Which kinds of features are available, and how many? | Features |
18 | For a given feature (e.g., a domain, PTM, or SNP), where is it in the sequence? | Features |
19 | For a given feature (e.g., a domain, PTM, or SNP), where is it in the structure? | Features & 3D Structure |
20 | For a given structure, where are a set of features located (e.g., all domains, PTMs, or SNPs)? | Features & 3D Structure |
21 | For each partner of a given protein, ... [repeat questions 1-20]? | 3D Structure |